Proline relative hydrophobicity

The third class of host defense peptides, the extended peptide class, is defined by the relative absence of a defined secondary structure. These peptides normally contain high proportions of amino acids such as histidine, tryptophan, or proline and tend to adopt an overall extended conformation upon interaction with hydrophobic environments. Examples of peptides belonging to the extended class include indolicidin, a bovine neutrophil peptide, and the porcine peptide fragment, tritpticin. These structures are stabilized by hydrogen bonding and van der Waals forces as a result of contact with lipids in contrast to the intramolecular stabilization forces found in the former peptide classes. 

In addition to the specific interactions described above, there is an important hydrophobic S2 binding site which accommodates the P2-proline residue. The number of non-bonded contacts made by atoms of the proline ring with atoms of this S2 binding site is relatively small - twelve compared to more than forty for the P2-tyrosine. The S3 binding site is formed by the two main chain hydrogen bonds from P3Ala (the NH and CO) to Gly 216 (CO-NH) in an approximately antiparallel sheet. 

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